#ALL - unique
size <- read.table("NC0001.trim_mm2_norepeat_nostrip.contigs_SOAP.table",header=T,sep="\t",row.names=1)
pdf("NC0001.norepeat_nostrip.feature_overlap_persize.pdf")
barplot(t(size),xlab="Read Length", ylab="Total # Reads", main="N.crassa unique matchers - by feature class and size",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=.1, end=.95),beside=F)
# ALL - non-unique
size <- read.table("NC0001.trim_mm2_repeat_strip.contigs_SOAP.table",header=T,sep="\t",row.names=1)
pdf("NC0001.repeat_strip.feature_overlap_persize.pdf")
barplot(t(size),xlab="Read Length", ylab="Total # Reads", main="N.crassa non-unique matchers - by feature class and size",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=0.1, end=0.95),beside=F)

# SS - unique
size <- read.table("NC0001.trim_mm2_norepeat_nostrip.contigs_SOAP.table_ss",header=T,sep="\t",row.names=1)
pdf("NC0001.norepeat_nostrip.feature_overlap_persize_ss.pdf")
barplot(t(size),xlab="Read Length", ylab="Total # Reads", main="N.crassa unique matchers - by feature class and size (same-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=.1, end=.95),beside=F)
# SS - non unique
size <- read.table("NC0001.trim_mm2_repeat_strip.contigs_SOAP.table_ss",header=T,sep="\t",row.names=1)
pdf("NC0001.repeat_strip.feature_overlap_persize_ss.pdf")
barplot(t(size),xlab="Read Length", ylab="Total # Reads", main="N.crassa non-unique matchers - by feature class and size (same-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=0.1, end=0.95),beside=F)

# OS - unique
size <- read.table("NC0001.trim_mm2_norepeat_nostrip.contigs_SOAP.table_os",header=T,sep="\t",row.names=1)
pdf("NC0001.norepeat_nostrip.feature_overlap_persize_os.pdf")
barplot(t(size),xlab="Read Length", ylab="Total # Reads", main="N.crassa unique matchers - by feature class and size (opp-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=.1, end=.95),beside=F)
# OS - nonunique
size <- read.table("NC0001.trim_mm2_repeat_strip.contigs_SOAP.table_os",header=T,sep="\t",row.names=1)
pdf("NC0001.repeat_strip.feature_overlap_persize_os.pdf")
barplot(t(size),xlab="Read Length", ylab="Total # Reads", main="N.crassa non-unique matchers - by feature class and size (opp-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=0.1, end=0.95),beside=F)

# ALL - unique
size <- read.table("NC0001.trim_mm2_norepeat_nostrip.contigs_SOAP.table_percent",header=T,sep="\t",row.names=1)
pdf("NC0001.norepeat_nostrip.class_size_classify_percent.pdf")
barplot(t(size),xlab="Read Length", ylab="Percentage of reads", main="N.crassa unique matchers - by feature class and size",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=.1, end=.95),beside=F)
# ALL - non-unique
size <- read.table("NC0001.trim_mm2_repeat_strip.contigs_SOAP.table_percent",header=T,sep="\t",row.names=1)
pdf("NC0001.repeat_strip.class_size_classify_percent.pdf")
barplot(t(size),xlab="Read Length", ylab="Percentage of reads", main="N.crassa non-unique matchers - by feature class and size",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=0.1, end=0.95),beside=F)

# percentage
# SS - unique
size <- read.table("NC0001.trim_mm2_norepeat_nostrip.contigs_SOAP.table_percent_ss",header=T,sep="\t",row.names=1)
pdf("NC0001.norepeat_nostrip.feature_overlap_persize_percent_ss.pdf")
barplot(t(size),xlab="Read Length", ylab="Percentage of reads", main="N.crassa unique matchers - by feature class and size (same-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=.1, end=.95),beside=F)
# SS - non-unique
size <- read.table("NC0001.trim_mm2_repeat_strip.contigs_SOAP.table_percent_ss",header=T,sep="\t",row.names=1)
pdf("NC0001.repeat_strip.feature_overlap_persize_percent_ss.pdf")
barplot(t(size),xlab="Read Length", ylab="Percentage of reads", main="N.crassa non-unique matchers - by feature class and size (same-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=0.1, end=0.95),beside=F)

# percentage
# OS - unique
size <- read.table("NC0001.trim_mm2_norepeat_nostrip.contigs_SOAP.table_percent_os",header=T,sep="\t",row.names=1)
pdf("NC0001.norepeat_nostrip.feature_overlap_persize_percent_os.pdf")
barplot(t(size),xlab="Read Length", ylab="Percentage of reads", main="N.crassa unique matchers - by feature class and size (opp-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=.1, end=.95),beside=F)
# OS - non-unique
size <- read.table("NC0001.trim_mm2_repeat_strip.contigs_SOAP.table_percent_os",header=T,sep="\t",row.names=1)
pdf("NC0001.repeat_strip.feature_overlap_persize_percent_os.pdf")
barplot(t(size),xlab="Read Length", ylab="Percentage of reads", main="N.crassa non-unique matchers - by feature class and size (opp-strand only)",space=0.1,cex.axis=0.8,las=1,cex=0.8,names=size$V1,legend=T,col=rainbow(7, start=0.1, end=0.95),beside=F)


